If I understand you correctly just mount the .iso with the loop option, add your files where you want them, and make a new .iso. Make a new checksum for it.
md5sum
sha256
Something like
Code:
mount -o loop youriso.iso /mounting/point
I think file-roller may do the same thing
You need to make a .iso of the install disk?
Code:
dd if=/dev/cdrom of=youriso.iso
Look at
mkisofs
K3b
Code:
cat /dev/cdrom > youriso.iso
Search LQ for making and buring .iso immages. Lots of threads on that.